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Homology Language

Homology Language. Biotechnology/Chemistry/Pharmaceutical Customer Partnership U.S. Patent and Trademark Office Arlington, Va July 29, 2003. Brian R. Stanton Quality Assurance Specialist Technology Center 1600 U.S. Patent and Trademark Office (703) 308-2801 brian.stanton@uspto.gov.

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Homology Language

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  1. Homology Language Biotechnology/Chemistry/Pharmaceutical Customer Partnership U.S. Patent and Trademark Office Arlington, Va July 29, 2003 Brian R. Stanton Quality Assurance Specialist Technology Center 1600 U.S. Patent and Trademark Office (703) 308-2801 brian.stanton@uspto.gov

  2. Language • % identical • Homology, identity, similarity • Hybridization

  3. Sample Claims • An isolated and purified nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO: 1. • An isolated and purified nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO: 1 wherein said nucleic acid encodes a protein having activity X.

  4. Sample Claims • An isolated and purified nucleic acid comprising a nucleotide sequence that is 90% identical to SEQ ID NO: 1. • An isolated and purified nucleic acid comprising a nucleotide sequence that is 90% identical to SEQ ID NO: 1, wherein said nucleic acid encodes a protein having activity X. • The specification provides sufficient support that isolated protein has a specific, substantial, and credible use related to activity X.

  5. Written Description • An isolated and purified nucleic acid comprising a nucleotide sequence that is 90% identical to SEQ ID NO: 1. • An isolated and purified nucleic acid comprising a nucleotide sequence that is 90% identical to SEQ ID NO: 1, wherein said nucleic acid encodes a protein having activity X.

  6. Functional language • If the specification provides sufficient support that the isolated protein has a specific, substantial, and credible use related to activity X, limiting the claims to proteins having activity X may help resolve a scope of enablement issue.

  7. Enablement • How to make? • How to find?

  8. Scope of enablement(some considerations) • Consensus sequences • State of the Art • Specification Support • Alignments? • Critical Residues • What to change and what not to change • Variations • What substitutions, deletions, insertions may be made? • Where can changes be made?

  9. Enablement: Claim language(some considerations) • Consensus sequence in claim? • Critical residues in claim? • e.g. An isolated and purified nucleic acid comprising a nucleotide sequences that is 90% identical to SEQ ID NO: 1, wherein said nucleic acid encodes a protein having activity X, and further wherein said nucleic acid includes SEQ ID NO: 2. • SEQ ID NO: 2 is the nucleotide sequence that encodes the catalytic domain (SEQ ID NO: 3) of a protein having activity X. • SEQ ID NO: 3 is sufficient to endow a protein with catalytic activity X.

  10. What % homology is appropriate? • Distinguish over prior art • Technology based • Do alignments yield information that suggests an appropriate amount of variation?

  11. Consensus Sequence Example A G C T T C C G G C T T A T A A A C G T A C T A T C C A G T A T A A A T A C T T ConsensusA x x x T C C x G x x T A x A x A C x T 11/20 = 55% homology between the two molecules. • Do they both have the desired function? • Are there teachings re: the permitted changes for the degenerate positions? • What is the homology at the amino acid level? • Are there teachings re: the permitted changes at the amino acid level?

  12. Enablement (cont.) • Assay • How to find? • How to screen for operative embodiments? • Wands analysis

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